SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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DOI：
10.1089/cmb.2012.0021
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发表时间：
2012-05-01
影响因子：
1.7
通讯作者：
Pevzner, Pavel A.
中科院分区：
文献类型：
--
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
各种环境中的大部分细菌无法在实验室中克隆，因此无法使用现有技术进行测序。单细胞基因组学的一个主要目标是用未培育生物的全基因组组合来补充以基因为中心的元基因组数据。由于高度不均匀的读取覆盖率以及测序错误和嵌合读取水平的增加，组装单细胞数据是具有挑战性的。我们描述了SPADS，这是一种用于单单元和标准(多单元)组装的新汇编器，并证明了它比最近发布的E+V-SC汇编器(专门用于单单元数据)和流行的汇编程序WELVET和SOAPdenovo(用于多单元数据)有所改进。Spade产生单细胞组合，提供关于不可培养细菌基因组的信息，远远超过通过传统的元基因组学研究可能获得的信息。黑桃可在线购买(http://bioinf.spbau.ru/spades).它以开源软件的形式分发。
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of un-cultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.